rs1923834

Positions:

• chr13-27786350-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0787 in 152,132 control chromosomes in the GnomAD database, including 521 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.079 (521 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0787 AC: 11966 AN: 152014 Hom.: 521 Cov.: 32

Gnomad AFR AF: 0.0910

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.0795

Gnomad ASJ AF: 0.0432

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.0549

Gnomad FIN AF: 0.0657

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0700

Gnomad OTH AF: 0.0673

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0787 AC: 11974 AN: 152132 Hom.: 521 Cov.: 32 AF XY: 0.0784 AC XY: 5836 AN XY: 74392

Gnomad4 AFR AF: 0.0910

Gnomad4 AMR AF: 0.0793

Gnomad4 ASJ AF: 0.0432

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.0551

Gnomad4 FIN AF: 0.0657

Gnomad4 NFE AF: 0.0700

Gnomad4 OTH AF: 0.0666

Alfa AF: 0.0702 Hom.: 658

Bravo AF: 0.0807

Asia WGS AF: 0.0900 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.61

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1923834; hg19: chr13-28360487;